I had the same problem one time. Turned out my 1/4" seam wasn't really 1/4" - it was between 1/4" and 3/8" (closer to 3/8"). I'd been using the edge of my presser foot as a guide, but had never checked to see if it was actually 1/4"! If your 1/4" seam is off by as little as 1/16" - whether wider or narrower - that can make 3/16" difference (almost 1/4") in the measurement of your block when you hae three seams.
The other possibility is an inaccurate ruler or perhaps cutting the strips just a little wider or narrower than 2-1/2". That also would throw off the measurements of the finished pieced square.
Good luck!